Plugboards have no effect on metadata being used to make collections, with the exception of title_sort and author_sort.

Put the tags you do not wish made into collections inside [ ] characters, as in [TODO.xxx.yyy].

You can also do it as you described, using a composite custom column 'built from other columns, behaves like tags'. I imagine that you would want to hide this column on the library view and not check the 'show in tag browser' box.